Entering edit mode
2.3 years ago
yufgua
•
0
Hi, I am just learning RNA-seq analysis, right now I am using STAR to build a genome index, however my code not working, Can anyone help me to check? with greeting:)
STAR
--runMode genomeGenerate
--genomeDir index
--runThreadN 10
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/GENOME --genomeFastaFiles
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.1.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.2.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.3.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.5.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.Mt.fa
--/Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.dna.chromosome.Pt.fa
--sjdbGTFfile /Users/felixguan/miniconda3/envs/RNA-seq/STAR/Arb/Arabidopsis_thaliana.TAIR10.54.gtf
--sjdbOverhang 99
What is the error? Usually one first concatenates all fasta files together and then runs star on that. Please show any error message. You will also need
\at the end of every but the last line if code is indeed in multiple lines.The
--at the beginning of the fasta file paths is probably breaking it too. In addition to concatenating the fasta files you can also provide them as space separated.